TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment.
Antineoplastic Agents
/ therapeutic use
Databases, Genetic
Datasets as Topic
Genetic Heterogeneity
High-Throughput Nucleotide Sequencing
Humans
Immunity, Innate
Immunotherapy
/ methods
Internet
Neoplasms
/ genetics
Quality Control
Single-Cell Analysis
/ methods
Software
Transcriptome
/ immunology
Tumor Cells, Cultured
Tumor Microenvironment
/ drug effects
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
08 01 2021
08 01 2021
Historique:
accepted:
16
10
2020
revised:
04
10
2020
received:
14
08
2020
pubmed:
13
11
2020
medline:
27
1
2021
entrez:
12
11
2020
Statut:
ppublish
Résumé
Cancer immunotherapy targeting co-inhibitory pathways by checkpoint blockade shows remarkable efficacy in a variety of cancer types. However, only a minority of patients respond to treatment due to the stochastic heterogeneity of tumor microenvironment (TME). Recent advances in single-cell RNA-seq technologies enabled comprehensive characterization of the immune system heterogeneity in tumors but posed computational challenges on integrating and utilizing the massive published datasets to inform immunotherapy. Here, we present Tumor Immune Single Cell Hub (TISCH, http://tisch.comp-genomics.org), a large-scale curated database that integrates single-cell transcriptomic profiles of nearly 2 million cells from 76 high-quality tumor datasets across 27 cancer types. All the data were uniformly processed with a standardized workflow, including quality control, batch effect removal, clustering, cell-type annotation, malignant cell classification, differential expression analysis and functional enrichment analysis. TISCH provides interactive gene expression visualization across multiple datasets at the single-cell level or cluster level, allowing systematic comparison between different cell-types, patients, tissue origins, treatment and response groups, and even different cancer-types. In summary, TISCH provides a user-friendly interface for systematically visualizing, searching and downloading gene expression atlas in the TME from multiple cancer types, enabling fast, flexible and comprehensive exploration of the TME.
Identifiants
pubmed: 33179754
pii: 5976978
doi: 10.1093/nar/gkaa1020
pmc: PMC7778907
doi:
Substances chimiques
Antineoplastic Agents
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
D1420-D1430Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
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